feat(aliby): add basic CLI

bin/run.py

+#!/usr/bin/env jupyter
+
+import argparse
+
+from aliby.pipeline import Pipeline, PipelineParameters
+
+parser = argparse.ArgumentParser(
+    prog="aliby-run", description="Run a default microscopy analysis pipeline"
+)
+
+param_values = {
+    "expt_id": None,
+    "distributed": 2,
+    "tps": 2,
+    "directory": "./data",
+    "filter": 0,
+    "host": None,
+    "username": None,
+    "password": None
+    # "overwrite": True,
+    # "earlystop": {
+    #     "min_tp": 100,
+    #     "thresh_pos_clogged": 0.4,
+    #     "thresh_trap_ncells": 8,
+    #     "thresh_trap_area": 0.9,
+    #     "ntps_to_eval": 5,
+    # },
+    # "logfile_level": "INFO",
+    # "use_explog": True,
+    # "use_logfile": False,
+}
+
+
+def _cast_str(x: str or None):
+    """
+    Cast string as int if possible. If Nonetype return None.
+    """
+    if x:
+        try:
+            return int(x)
+        except:
+            return x
+
+
+for k in param_values:
+    parser.add_argument(f"--{k}", action="store")
+
+args = parser.parse_args()
+
+for k in param_values:
+    if passed_value := _cast_str(getattr(args, k)):
+
+        param_values[k] = passed_value
+
+params = PipelineParameters.default(general=param_values)
+p = Pipeline(params)
+
+p.run()